-
Basic run of
BiocCheck('BgeeCall')
on the package* ERROR: Packages providing 1 object(s) used in this package should be imported in the NAMESPACE file, otherwise packages importing this package may fail. package::object in function() graphics::mtext in plot_distributions()
-
File size too big, software packages need to be 5MB in size or less. Please check "BFG cleaner".
* Checking individual file sizes... * WARNING: The following files are over 5MB in size: '.git/objects/pack/pack-94ca9deb2be0a9e6fc630aa9c82ad98cb3dfbb24.pack'
-
Other issues,
* Checking for valid maintainer...
* WARNING: Use Authors@R (preferred) or Author/Maintainer fields
not both.
* Checking DESCRIPTION/NAMESPACE consistency...
* WARNING: Import BgeeDB in NAMESPACE as well as DESCRIPTION.
* Checking vignette directory...
This is a software package
* WARNING: Vignette[s] still using 'VignetteIndexEntry{Vignette
Title}' Update the following files from using template values:
bgeecall-manual.Rmd
- Coding practice issues,
* Checking coding practice...
* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
retrieveFromCommunity.R (line 27, column 27)
retrieveFromCommunity.R (line 44, column 31)
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
create_kallisto_index.Rd, generate_calls_workflow.Rd,
Please run BiocCheck('BgeeCall')
on the package and make the
appropriate changes. Install the package BiocCheck
and run the
function. We cannot make the change without fixing the issues given
above.
You end up getting,
Summary:
ERROR count: 1
WARNING count: 5
NOTE count: 8
ok
ok
Hello Julien,
A few of things,
You need to update your Bioconductor repo as well. We'll just use that to check your package and code for review. I need know which repo I should review, because last time I just reviewed the Bioconductor Git version of your package.
Pay attention to the version numbers. Your GitHub repo is not in sync with your Bioconductor git repo. Make sure the devel branch is updated with an appropriate version number 1.3.0 (It has to be odd). It needs the commits which were made by the Bioconductor Core team.
Errors your package on Github generates,
End-User messages
• message() communicates diagnostic messages (e.g., progress during lengthy computations) during code evaluation.
• warning() communicates unusual situations handled by your code.
• stop() indicates an error condition.
• cat() or print() are used only when displaying an object to the user, e.g., in a show method.
Just throw a warning(), don't imitate it with cat(paste0())
When you use
stop()
So, you don't need to write "ERROR"
Your code will print out
Error:ERROR.....
error
argumenteg:
tryCatch(stop(e), error = function(e) e, finally = print("Hello"))
When calling
Kallisto
please usesystem2
instead of thesystem
calls. It is more robust. Do this all across your package.Instead of this,
if (removeFile == TRUE)
you can just sayif(removeFile)
. It will evaluate the logical operation.This code won't evaluate, you want the spelling "Darwin"
Please make sure the comments i've provided are corrected package wide if there are multiple instances of the same issue.
Thanks,
Nitesh